Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

A quality control algorithm for DNA sequencing projects

O White1, T Dunning, G Sutton

  • 1Institute for Genomic Research, Gaithersburg, MD 20878.

Nucleic Acids Research
|August 11, 1993
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

N-acetyl-L-leucine for Niemann-Pick type C: a multinational double-blind randomized placebo-controlled crossover study.

Trials·2023
Same author

Comparison of carcinogenic potency across life stages: implications for the assessment of transplacental cancer risk.

Journal of toxicology and environmental health. Part A·2019
Same author

The Boltzmann project.

Metrologia·2019
Same author

Primary care REFerral for EchocaRdiogram (REFER) in heart failure: a diagnostic accuracy study.

The British journal of general practice : the journal of the Royal College of General Practitioners·2016
Same author

Enterobacter aerogenes Hormaeche and Edwards 1960 (Approved Lists 1980) and Klebsiella mobilis Bascomb et al. 1971 (Approved Lists 1980) share the same nomenclatural type (ATCC 13048) on the Approved Lists and are homotypic synonyms, with consequences for the name Klebsiella mobilis Bascomb et al. 1971 (Approved Lists 1980).

International journal of systematic and evolutionary microbiology·2016
Same author

Estimates of the difference between thermodynamic temperature and the International Temperature Scale of 1990 in the range 118 K to 303 K.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences·2016
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

A new statistical test identifies DNA contamination by analyzing hexamer composition, even for unknown organisms. This method revealed yeast and bacterial DNA in human expressed sequence tag datasets.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • DNA and RNA libraries can be contaminated by heterologous sequences from various sources.
  • Current detection methods like hybridization and sequence alignment have limitations in identifying unknown contaminants.

Purpose of the Study:

  • To develop a novel statistical method for detecting heterologous DNA sequence contamination.
  • To evaluate the utility of this method for quality control of public expressed sequence tag (EST) datasets.

Main Methods:

  • Developed a statistical test based on differences in hexamer composition between DNA sequences of different organisms.
  • Applied the test to major public EST datasets, including human, C.elegans, yeast, and bacterial sequences.
  • Confirmed findings using traditional similarity searches.

Related Experiment Videos

Main Results:

  • The hexamer composition test effectively identifies heterologous DNA sequences without needing a reference database.
  • Detected heterogeneity in human and C.elegans EST datasets, though not clearly linked to cross-species contamination.
  • Found direct evidence of yeast and bacterial sequence contamination in some human-annotated ESTs.

Conclusions:

  • The hexamer composition test is a powerful tool for identifying DNA contamination, including from previously unknown organisms.
  • This method serves as a valuable quality control and peer evaluation tool for genomic datasets.
  • Publicly available EST data may contain significant cross-contamination, necessitating rigorous quality assessment.